Is Their Any Good Tool For The De Novo Assembly Of Chimeric Reads

Question

[Raghav]

Hello you all, I am looking for good de novo assembly tool for illumina paired end reads [100 nt long],

Your suggestions are always welcome. Thank you

[Michael]

how do you know your reads are chimeric? Are you sure that you are using chimeric in the correct sense?

[Raghav]

Dear, Michael First I tried to mapped entire reads on reference and then filter chimeric reads only. yes, I am sure. if you have any suggestion regarding this then your are most welcome.

[Tky]

[100 nt long] should be [100 bp long]

[Raghav]

thnQ for correcting it.

[Manu Prestat]

Are you talking about chimera potentially resulting from a PCR step? In that case, you should think about filtering out those which are detected using an algo such as, e.g. uChime http://drive5.com/usearch/manual/uchime_algo.html before the assembly step.

Answer 1

[Vivek]

It depends on the genome size and insert sizes of the reads. For larger genomes, if you have one overlapping insert library and another large insert library, you can use ALLPATHS which has inbuilt error correction mechanism that can handle chimeric reads. Otherwise you have SOAP-Denovo, which is pretty efficient but you need to develop your own error correction scripts to remove chimeric reads before assembly.

[Raghav]

Dear Vivek, ThnQ for the suggestion, I think SOAP-Denovo is realy good one for de novo assembly.